Table 3.
Comparative Genotype Analysis Using the Mouse Diversity Array
| 129S6 vs B6 | 129S6 vs 129 S1 | 129S6 vs LP/J | 129S1 vs LP/J | 129S1 vs B6 | B6 vs LP/J | |
|---|---|---|---|---|---|---|
| Genome wide | ||||||
| Number of mismatches | 115,069 | 4508 | 41,949 | 38,908 | 114,567 | 116,926 |
| Percentage of mismatches | 21.22% | 0.83% | 7.74% | 7.18% | 21.13% | 21.57% |
| Percentage of matches | 78.78% | 99.17% | 92.26% | 92.82% | 78.87% | 78.43% |
| Percentage of IBD∗ | 27.42% | 96.69% | 72.16% | 74.43% | 28.04% | 27.99% |
| 129S6 and 129S1 non-IBD† | ||||||
| Number of mismatches | 4075 | 4048 | 3931 | 1100 | 3641 | 3481 |
| Percentage of mismatches | 23.01% | 22.85% | 22.19% | 6.21% | 20.56% | 19.56% |
Six pairwise genotype comparisons of four inbred mouse strains were performed at 542,190 SNPs distributed across the genome to assess the extent of genetic relatedness.
∗
The fraction of the genome that was defined as identical by descent (IBD) between any two strains was determined by calculating the percentage of those two genomes with 98% or greater identity over windows of 100 SNPs.
†
The regions of the genome that were non-IBD between 129 S6 and 129 S1 contained 17,713 SNPs of the Mouse Diversity Array. Pairwise genotype comparisons of the four inbred mouse strains were performed at these 17,713 SNPs to assess the genetic relatedness within the 129 S6 and 129 S1 non-IBD regions.